Normalized L3-based link prediction in protein-protein interaction networks.

BACKGROUND: Protein-protein interaction (PPI) data is an important type of data used in functional genomics. However, high-throughput experiments are often insufficient to complete the PPI interactome of different organisms. Computational techniques are thus used to infer missing data, with link prediction being one such approach that uses the structure of the network of PPIs known so far to identify non-edges whose addition to the network would make it more sound, according to some underlying assumptions. Recently, a new idea called the L3 principle introduced biological motivation into PPI link predictions, yielding predictors that are superior to general-purpose link predictors for complex networks. Interestingly, the L3 principle can be interpreted in another way, so that other signatures of PPI networks can also be characterized for PPI predictions. This alternative interpretation uncovers candidate PPIs that the current L3-based link predictors may not be able to fully capture, underutilizing the L3 principle. RESULTS: In this article, we propose a formulation of link predictors that we call NormalizedL3 (L3N) which addresses certain missing elements within L3 predictors in the perspective of network modeling. Our computational validations show that the L3N predictors are able to find missing PPIs more accurately (in terms of true positives among the predicted PPIs) than the previously proposed methods on several datasets from the literature, including BioGRID, STRING, MINT, and HuRI, at the cost of using more computation time in some of the cases. In addition, we found that L3-based link predictors (including L3N) ranked a different pool of PPIs higher than the general-purpose link predictors did. This suggests that different types of PPIs can be predicted based on different topological assumptions, and that even better PPI link predictors may be obtained in the future by improved network modeling.

Metronidazole-modified Au@BSA nanocomposites for dual sensitization of radiotherapy in solid tumors.

The hypoxic microenvironment of solid tumors can lead to reduced therapeutic DNA damage to the tumor cells, thus diminishing tumor sensitivity to radiotherapy. Although hypoxic radiosensitizers can improve radiotherapy efficacy by enhancing the role of oxygen, their effects are limited by the uneven distribution of oxygen within solid tumor tissues. In this study, a novel radiosensitizer via leveraging gold complexes and metronidazole (MN) was synthesized to improve radiotherapeutic efficacy. The gold atoms incorporated in the radiosensitizer enabled efficient deposition of high-energy radiation; the hydrophobic metronidazole was reduced to hydrophilic aminoimidazole under hypoxia conditions and further promoted radiotherapy sensitization. The results of CCK-8 assays, Live/Dead assays, γ-H2AX immunofluorescence indicated that metronidazole-modified Au@BSA nanocomposites (NCs) exhibited excellent antitumor effects. The in vivo antitumor tests further showed an inhibition rate of 100%. These results demonstrated that the NCs successfully enhanced radiotherapy efficacy by the dual sensitization strategy. Overall, we believe this multimodal radiosensitizing nanocomplex can significantly inhibit tumor growth and metastasis, with their hypoxia-oriented characteristics ensuring a higher efficacy and safety.

A differential-targeting core-shell microneedle patch with coordinated and prolonged release of mangiferin and MSC-derived exosomes for scarless skin regeneration.

Microneedles for skin regeneration are conventionally restricted by uncontrollable multi-drug release, limited types of drugs, and poor wound adhesion. Here, a novel core-shell microneedle patch is developed for scarless skin repair, where the shell is composed of hydrophilic gelatin methacryloyl (GelMA) loaded with mangiferin, an anti-inflammatory small molecule, and the core is composed of hydrophobic poly (lactide-co-propylene glycol-co-lactide) dimethacrylates (PGLADMA) loaded with bioactive macromolecule and human mesenchymal stromal cell (hMSC)-derived exosomes. This material choice provides several benefits: the GelMA shell provides a swelling interface for tissue interlocking and rapid release of mangiferin at an early wound healing stage for anti-inflammation, whereas the PGLADMA core offers long-term encapsulation and release of exosomes (30% release in 3 weeks), promoting sustained angiogenesis and anti-inflammation. Our results demonstrate that the core-shell microneedle possesses anti-inflammatory properties and can induce angiogenesis both in vitro in terms of macrophage polarization and tube formation of human umbilical vein endothelial cells (HUVECs), and in vivo in terms of anti-inflammation, re-epithelization, and vessel formation. Importantly, we also observe reduced scar formation in vivo. Altogether, the degradation dynamics of our hydrophilic/hydrophobic materials enable the design of a core-shell microneedle for differential and prolonged release, promoting scarless skin regeneration, with potential for other therapies of long-term exosome release.

Correction: A differential-targeting core-shell microneedle patch with coordinated and prolonged release of mangiferin and MSC-derived exosomes for scarless skin regeneration.

Correction for 'A differential-targeting core-shell microneedle patch with coordinated and prolonged release of mangiferin and MSC-derived exosomes for scarless skin regeneration' by Shang Lyu et al., Mater. Horiz., 2024, https://doi.org/10.1039/D3MH01910A.

Going below and beyond the surface: Microneedle structure, materials, drugs, fabrication, and applications for wound healing and tissue regeneration.

Microneedle, as a novel drug delivery system, has attracted widespread attention due to its non-invasiveness, painless and simple administration, controllable drug delivery, and diverse cargo loading capacity. Although microneedles are initially designed to penetrate stratum corneum of skin for transdermal drug delivery, they, recently, have been used to promote wound healing and regeneration of diverse tissues and organs and the results are promising. Despite there are reviews about microneedles, few of them focus on wound healing and tissue regeneration. Here, we review the recent advances of microneedles in this field. We first give an overview of microneedle system in terms of its potential cargos (e.g., small molecules, macromolecules, nucleic acids, nanoparticles, extracellular vesicle, cells), structural designs (e.g., multidrug structures, adhesive structures), material selection, and drug release mechanisms. Then we briefly summarize different microneedle fabrication methods, including their advantages and limitations. We finally summarize the recent progress of microneedle-assisted wound healing and tissue regeneration (e.g., skin, cardiac, bone, tendon, ocular, vascular, oral, hair, spinal cord, and uterine tissues). We expect that our article would serve as a guideline for readers to design their microneedle systems according to different applications, including material selection, drug selection, and structure design, for achieving better healing and regeneration efficacy.

Living prosthetic breast for promoting tissue regeneration and inhibiting tumor recurrence.

Developing a living prosthetic breast to inhibit potential breast cancer recurrence and simultaneously promote breast reconstruction would be a promising strategy for clinical treatment of breast cancer after mastectomy. Here, a living prosthetic breast in the form of injectable gelatin methacryloyl microspheres is prepared, where they encapsulated zeolitic imidazolate framework (ZIF) nanoparticles loaded with small molecules urolithin C (Uro-C) and adipose-derived stem cells (ADSCs). Taking advantage of the acidic tumor microenvironment, the ZIF triggered a pH-sensitive drug release in situ so that Uro-C can induce tumor cell apoptosis via reactive oxygen species (ROS) generation. Meanwhile, the ADSCs proliferate in situ to promote tissue regeneration. Using such a design, our data showed that the ADSCs maintained viable and proliferate under the inhibitory effect of Uro-C in vitro. Through ROS generation, Uro-C also activated a suppressive tumor microenvironment in mice by both re-polarizing M2 macrophages to M1 macrophages for elevated inflammatory responses, and increasing the ratio between CD8 and CD4 T cells for tumor recurrence inhibition, significantly promoting new adipose tissue formation. Altogether, our results demonstrate that the prepared living prosthetic breast with bifunctional properties can be a promising candidate in clinic involving tumor treatment and tissue engineering in synergy.

Petite miracles: insight into the nano-management of scarless wound healing.

Scars affect millions of patients worldwide, yet their treatment efficacy and options clinically remain limited. In recent years, increased understanding of scar formation pathways leading to developments in nanotechnology have opened many opportunities for scar detection, prevention, and treatment due to the nanoscale features and therapeutic delivery capabilities of such technologies. Led by nanoparticles (NPs) and nanofibers, these novel strategies can aid in reducing scar contracture, improving wound-healing efficacy, and advancing progress towards scarless wound healing.